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<p>Understanding the biogeochemical patterns of microbial diversity and community structure is still challenging in Himalayan Lake ecosystems. Advanced molecular approaches such as environmental DNA (eDNA) that offer rapid and efficient insights into biodiversity distribution and abundance with high sensitivity are required for biomonitoring bacterial populations in such ecosystems. Therefore, the present study evaluated the taxonomic and functional diversity of bacterial communities in Dal Lake using eDNA and whole metagenomic sequencing. Taxonomic annotations in Dal Lake revealed <i>Proteobacteria</i> as the dominant taxa with the highest relative abundance reported from Dalgate basin (69.53%), Nishat basin (67.44%), Hazratbal basin (65.03%), Nigeen basin (61.71%), and Gagribal basin (51.71%) followed by <i>Bacteriodetes, Actinobacteria</i> and <i>Planctomycetes</i>. Similarly, functional annotations employing KEGG analysis revealed cellular metabolism, membrane transport, environmental and genetic information, and amino acid metabolism as abundant metagenome functions, while COG analysis showed general function prediction, amino acid transport and metabolism, and defense mechanisms as dominant functions. Dominant Pfam annotations across the basins included ABC transporters, response regulator receiver domain, short chain dehydrogenase, AMP-binding enzyme, Acyl-CoA dehydrogenase, C-terminal domain. Physico-chemical analysis in Dal Lake basins was also undertaken to define the pollution levels that influence the growth and biological activities of bacterial communities. The observed trends in consonance with principal component analysis revealed that variance is maximally explained by pH, nitrates, total hardness and total alkalinity (55.34%) followed by chlorides, total phosphorus and dissolved oxygen (29.34%). Canonical correspondence analysis indicated <i>Planctomycetes</i> and <i>Proteobacteria</i> contributed evenly across environmental variables, with Hazratbal basin exhibiting a balanced bacterial community structure. Similarly, electrical conductivity and chlorides affect the composition of microbial communities in the Dalgate basin and nitrates in the Nigeen and Nishat basins, respectively.</p> Graphical abstract <p></p>

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Taxonomic and functional annotations of microbial communities in relation to environmental factors in a Himalayan freshwater lake using environmental DNA and metagenomics

  • 期刊论文

  • 发表日期：

    2025年7月3日

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  • Shahnawaz Hassan,
  • Bikram Singh Bali,
  • Wani Muneer,
  • Muzafar Zaman,
  • Aarif Yaseen,
  • Bashir Ahmad Ganai

摘要

Understanding the biogeochemical patterns of microbial diversity and community structure is still challenging in Himalayan Lake ecosystems. Advanced molecular approaches such as environmental DNA (eDNA) that offer rapid and efficient insights into biodiversity distribution and abundance with high sensitivity are required for biomonitoring bacterial populations in such ecosystems. Therefore, the present study evaluated the taxonomic and functional diversity of bacterial communities in Dal Lake using eDNA and whole metagenomic sequencing. Taxonomic annotations in Dal Lake revealed Proteobacteria as the dominant taxa with the highest relative abundance reported from Dalgate basin (69.53%), Nishat basin (67.44%), Hazratbal basin (65.03%), Nigeen basin (61.71%), and Gagribal basin (51.71%) followed by Bacteriodetes, Actinobacteria and Planctomycetes. Similarly, functional annotations employing KEGG analysis revealed cellular metabolism, membrane transport, environmental and genetic information, and amino acid metabolism as abundant metagenome functions, while COG analysis showed general function prediction, amino acid transport and metabolism, and defense mechanisms as dominant functions. Dominant Pfam annotations across the basins included ABC transporters, response regulator receiver domain, short chain dehydrogenase, AMP-binding enzyme, Acyl-CoA dehydrogenase, C-terminal domain. Physico-chemical analysis in Dal Lake basins was also undertaken to define the pollution levels that influence the growth and biological activities of bacterial communities. The observed trends in consonance with principal component analysis revealed that variance is maximally explained by pH, nitrates, total hardness and total alkalinity (55.34%) followed by chlorides, total phosphorus and dissolved oxygen (29.34%). Canonical correspondence analysis indicated Planctomycetes and Proteobacteria contributed evenly across environmental variables, with Hazratbal basin exhibiting a balanced bacterial community structure. Similarly, electrical conductivity and chlorides affect the composition of microbial communities in the Dalgate basin and nitrates in the Nigeen and Nishat basins, respectively.

Graphical abstract